4WX2

Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with two F6F molecules in the alpha-site and one F6F molecule in the beta-site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KKXPDB entry 4KKX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.829850 mM Bicine-NaOH, pH 7.8; 10% PEG 8,000; 2 mM spermine
Crystal Properties
Matthews coefficientSolvent content
2.5351.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.809α = 90
b = 58.89β = 95.21
c = 67.27γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7520.9599.90.079.93.5724027240221.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.841000.4612.13.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4KKX1.7520.9572402360199.890.16030.15840.1885RANDOM26.729
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.310.040.10.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.516
r_dihedral_angle_4_deg18.697
r_dihedral_angle_3_deg12.696
r_dihedral_angle_1_deg5.764
r_mcangle_it2.284
r_angle_refined_deg1.721
r_mcbond_it1.484
r_mcbond_other1.473
r_angle_other_deg0.872
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.516
r_dihedral_angle_4_deg18.697
r_dihedral_angle_3_deg12.696
r_dihedral_angle_1_deg5.764
r_mcangle_it2.284
r_angle_refined_deg1.721
r_mcbond_it1.484
r_mcbond_other1.473
r_angle_other_deg0.872
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4905
Nucleic Acid Atoms
Solvent Atoms617
Heterogen Atoms90

Software

Software
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
SCALAdata scaling
iMOSFLMdata reduction
CrystalCleardata collection
d*TREKdata reduction
SCALEPACKdata scaling